Personally, I'd go with the Juan Valdez cafes in Medellin and Bogota. In particular, I found the Juan Valdez cafe that was across the street from Parque 93 in Bogota to be the most pleasant place to sit.
Wow! that is quite a broad question... Certainly the Colombian coffee drinkers might have a totally different taste for coffee than the Brazilians, etc... I had a great cup of coffee in Juan Valdez in Bogota (several locations). Beats Starbucks hands down. You go there for the coffee.
Confeitaria Colombo in Rio de Janeiro is not to be missed. The atmosphere is turn of the century Belle Epoque and has been popular among Rio's literary Intelligentsia since 1894. Jill www.SouthAmericanEscapes.com/blog